Some parts of my project aren't saved in the .blend file
Blender does not save unused datablocks you need to add a fake user to store datablocks that are not in use. See DataSystem Sections Users and Fake User

The setting of mip-maps is not stored in a .blend file you would need to save the user-preferences in the same dialog (button in the lower left corner).

Related:

What does &quot;users&quot; means in term of datablocks?